Bacterial Classification of Fish-Pathogenic Mycobacterium Species by Multigene Phylogenetic Analyses and MALDI Biotyper Identification System

Marine Biotechnology

Volumn 15, Issue 3, 2013, Pages 340-348

  Kurokawa, Satoru ^a   Kabayama, Jun ^a   Fukuyasu, Tsuguaki ^a   Hwang, Seong Don ^b   Park, Chan Il ^b   Park, Seong Bin ^b   del Castillo, Carmelo S ^b   Hikima, Jun ichi ^b   Jung, Tae Sung ^b   Kondo, Hidehiro ^c   Hirono, Ikuo ^c   Takeyama, Haruko ^d   Aoki, Takashi ^b,d  

^a Meiji Seika Pharma   (Japan)

^b Gyeongsang National University   (South Korea)

^c TOKYO UNIVERSITY OF MARINE SCIENCE AND TECHNOLOGY   (Japan)

^d WASEDA UNIVERSITY   (Japan)

Author keywords

MALDI Biotyper; Mycobacterium marinum; Mycobacterium sp.; Phylogenetic analysis

Indexed keywords

GENES; MASS SPECTROMETRY; RNA; SILVER COMPOUNDS;

BACTERIAL CLASSIFICATIONS; BIOCHEMICAL METHODS; BIOTYPER; MATRIX ASSISTED LASER DESORPTION IONIZATION; MYCOBACTERIUM MARINUM; MYCOBACTERIUM SP; PATHOGENIC MYCOBACTERIA; PHYLOGENETIC ANALYSIS;

FISH;

BACTERIUM; FISH; IDENTIFICATION METHOD; PATHOGEN; PHYLOGENETICS; PHYLOGENY; PROTEOMICS; SUBSPECIES; TAXONOMY;

EUROPE; JAPAN; THAILAND;

BACTERIA (MICROORGANISMS); MYCOBACTERIUM; MYCOBACTERIUM MARINUM; MYCOBACTERIUM SP.;

PRIMER DNA;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; BACTERIAL GENE; CLASSIFICATION; CLUSTER ANALYSIS; DNA SEQUENCE; EUROPE; FISH; GENETICS; JAPAN; MASS SPECTROMETRY; METHODOLOGY; MICROBIOLOGY; MOLECULAR GENETICS; MYCOBACTERIUM MARINUM; NUCLEOTIDE SEQUENCE; PHYLOGENY; SPECIES DIFFERENCE; THAILAND;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CLUSTER ANALYSIS; DNA PRIMERS; EUROPE; FISHES; GENES, BACTERIAL; JAPAN; MOLECULAR SEQUENCE DATA; MYCOBACTERIUM MARINUM; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; THAILAND;

EID: 84876189007     PISSN: 14362228     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10126-012-9492-x     Document Type: Article

References (52)

1. Arjomandzadegan M, Owlia P, Ranjbar R, Farazi AA, Sofian M, Sadrnia M, Surkova LK, Titov LP (2011) Rapid and simple approach for identification of Mycobacterium tuberculosis and M. bovis by detection of regulatory gene whiB7. Acta Microbiol Immunol Hung 58: 65-74.
2. Backman S, Ferguson HW, Prescott JF, Wilcock BP (1990) Progressive panophthalmitis in chinook salmon, Oncorhynchus tshawytscha (Walbaum): a case report. J Fish Dis 13: 345-353.
3. Bessede E, Solecki O, Sifre E, Labadi L, Megraud F (2011) Identification of Campylobacter species and related organisms by matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry. Clin Microbiol Infect 17: 1735-1739.
4. Bille E, Dauphin B, Leto J, Bougnoux ME, Beretti JL, Lotz A, Suarez S, Meyer J, Join-Lambert O, Descamps P, Grall N, Mory F, Dubreuil L, Berche P, Nassif X, Ferroni A (2012) MALDI-TOF MS Andromas strategy for the routine identification of bacteria, mycobacteria, yeasts, Aspergillus spp. and positive blood cultures. Clin Microbiol Infect 18: 1117-1125.
5. Bizzini A, Durussel C, Bille J, Greub G, Prod'hom G (2010) Performance of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of bacterial strains routinely isolated in a clinical microbiology laboratory. J Clin Microbiol 48: 1549-1554.
6. Blackwood KS, He C, Gunton J, Turenne CY, Wolfe J, Kabani AM (2000) Evaluation of recA sequences for identification of Mycobacterium species. J Clin Microbiol 38: 2846-2852.
7. Bottger EC (1991) Systematics, differentiation, and detection of bacterial infections-the family Mycobacteriaceae. Immun infekt 19: 143-152.
8. Brennan PJ, Nikaido H (1995) The envelope of mycobacteria. Annu Rev Biochem 64: 29-63.
9. Brunello F, Ligozzi M, Cristelli E, Bonora S, Tortoli E, Fontana R (2001) Identification of 54 mycobacterial species by PCR-restriction fragment length polymorphism analysis of the hsp65 gene. J Clin Microbiol 39: 2799-2806.
10. Cherkaoui A, Hibbs J, Emonet S, Tangomo M, Girard M, Francois P, Schrenzel J (2010) Comparison of two matrix-assisted laser desorption ionization-time of flight mass spectrometry methods with conventional phenotypic identification for routine identification of bacteria to the species level. J Clin Microbiol 48: 1169-1175.
11. Cloud JL, Neal H, Rosenberry R, Turenne CY, Jama M, Hillyard DR, Carroll KC (2002) Identification of Mycobacterium spp. by using a commercial 16S ribosomal DNA sequencing kit and additional sequencing libraries. J Clin Microbiol 40: 400-406.
12. Devulder G, Perouse de Montclos M, Flandrois JP (2005) A multigene approach to phylogenetic analysis using the genus Mycobacterium as a model. Int J Syst Evol Microbiol 55: 293-302.
13. Eigner U, Holfelder M, Oberdorfer K, Betz-Wild U, Bertsch D, Fahr AM (2009) Performance of a matrix-assisted laser desorption ionization-time-of-flight mass spectrometry system for the identification of bacterial isolates in the clinical routine laboratory. Clin Lab 55: 289-296.
14. El Khéchine A, Couderc C, Flaudrops C, Raoult D, Drancourt M (2011) Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identification of mycobacteria in routine clinical practice. PLoS One 6: e24720.
15. Ferroni A, Suarez S, Beretti JL, Dauphin B, Bille E, Meyer J, Bougnoux ME, Alanio A, Berche P, Nassif X (2010) Real-time identification of bacteria and Candida species in positive blood culture broths by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 48: 1542-1548.
16. Gauthier DT, Helenthal AM, Rhodes MW, Vogelbein WK, Kator HI (2011) Characterization of photochromogenic Mycobacterium spp. from Chesapeake Bay striped bass Morone saxatilis. Dis Aquat Organ 195: 113-124.
17. Ghittino C, Latini M, Agnetti F, Panzieri C, Lauro L, Ciappelloni R, Petracca G (2003) Emerging pathologies in aquaculture: effects on production and food safety. Vet Res Commun 27: 471-479.
18. Gingeras TR, Ghandour G, Wang E, Berno A, Small PM, Drobniewski F, Alland D, Desmond E, Holodniy M, Drenkow J (1998) Simultaneous genotyping and species identification using hybridization pattern recognition analysis of generic Mycobacterium DNA arrays. Genome Res 8: 435-448.
19. Hedrick RP, McDowell T, Groff J (1987) Mycobacteriosis in cultured striped bass from California. J Wildlife Dis 23: 391-395.
20. Kasai H, Ezaki T, Harayama S (2000) Differentiation of phylogenetically related slowly growing mycobacteria by their gyrB sequences. J Clin Microbiol 38: 301-308.
21. Kim BJ, Lee SH, Lyu MA, Kim SJ, Bai GH, Chae GT, Kim EC, Cha CY, Kook YH (1999) Identification of mycobacterial species by comparative sequence analysis of the RNA polymerase gene (rpoB). J Clin Microbiol 37: 1714-1720.
22. Kirschner P, Bottger EC (1998) Species identification of mycobacteria using rDNA sequencing. Meth Mol Biol 101: 349-361.
23. Knibb W, Colorni A, Ankaoua M, Lindell D, Diamant A, Gordin H (1993) Detection and identification of a pathogenic marine Mycobacterium from the European seabass Dicentrarchus labrax using polymerase chain reaction and direct sequencing of 16S rDNA sequences. Mol Mar Biol Biotechnol 2: 225-232.
24. Kolbert CP, Persing DH (1999) Ribosomal DNA sequencing as a tool for identification of bacterial pathogens. Curr Opin Microbiol 2: 299-305.
25. Kusuda R, Inoue M, Sugiura H, Kawai K (1993) Characteristics of a pathogenic mycobacterium sp. isolated from cultured striped jack, Pseudocaranx dentex. Aquac Sci 41: 125-131.
26. Kusuda R, Kawakami K, Kawai K (1987) A fish-pathogenic Mycobacterium sp. isolated from an epizootic of cultured yellowtail. Nippon Suisan Gakk 53: 1797-1804 (in Japanese).
27. La Scola B, Raoult D (2009) Direct identification of bacteria in positive blood culture bottles by matrix-assisted laser desorption ionisation time-of-flight mass spectrometry. PLoS One 4: e8041.
28. Lewis S, Chinabut S (2011) Mycobacteriosis and nocardiosis. In: Woo PTK, Bruno DW, editors. Fish disease and disorders. 2nd edn. Cambridge, MA: CABI Pub-UK, Wallingford, p. 397-423.
29. Liu J, Rosenberg EY, Nikaido H (1995) Fluidity of the lipid domain of cell wall from Mycobacterium chelonae. Proc Natl Acad Sci USA 92: 11254-11258.
30. Lotz A, Ferroni A, Beretti JL, Dauphin B, Carbonnelle E, Guet-Revillet H, Veziris N, Heym B, Jarlier V, Gaillard JL, Pierre-Audigier C, Frapy E, Berche P, Nassif X, Bille E (2010) Rapid identification of mycobacterial whole cells in solid and liquid culture media by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 48: 4481-4486.
31. Marvin LF, Roberts MA, Fay LB (2003) Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in clinical chemistry. Clin Chim Acta 337: 11-21.
32. Nguyen L, Thompson CJ (2006) Foundations of antibiotic resistance in bacterial physiology: the mycobacterial paradigm. Trends Microbiol 14: 304-312.
33. Noga E (1996) Fish Disease. Mosby-Year Book, Inc, St. Louis.
34. Pai S, Esen N, Pan X, Musser JM (1997) Routine rapid Mycobacterium species assignment based on species-specific allelic variation in the 65-kilodalton heat shock protein gene (hsp65). Arch Pathol Lab Med 121: 859-864.
35. Ringuet H, Akoua-Koffi C, Honore S, Varnerot A, Vincent V, Berche P, Gaillard JL, Pierre-Audigier C (1999) Hsp65 sequencing for identification of rapidly growing mycobacteria. J Clin Microbiol 37: 852-857.
36. Rogall T, Flohr T, Bottger EC (1990) Differentiation of Mycobacterium species by direct sequencing of amplified DNA. J Gen Microbiol 136: 1915-1920.
37. Roth A, Fischer M, Hamid ME, Michalke S, Ludwig W, Mauch H (1998) Differentiation of phylogenetically related slowly growing mycobacteria based on 16S-23S rRNA gene internal transcribed spacer sequences. J Clin Microbiol 36: 139-147.
38. Saleeb PG, Drake SK, Murray PR, Zelazny AM (2011) Identification of mycobacteria in solid-culture media by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 49: 1790-1794.
39. Sauer S, Kliem M (2010) Mass spectrometry tools for the classification and identification of bacteria. Nat Rev Microbiol 8: 74-82.
40. Schmidt V, Jarosch A, Marz P, Sander C, Vacata V, Kalka-Moll W (2012) Rapid identification of bacteria in positive blood culture by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Eur J Clin Microbiol Infect Dis 31: 311-317.
41. Seng P, Drancourt M, Gouriet F, La Scola B, Fournier PE, Rolain JM, Raoult D (2009) Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Infect Dis 49: 543-551.
42. Shitikov E, Ilina E, Chernousova L, Borovskaya A, Rukin I, Afanas'ev M, Smirnova T, Vorobyeva A, Larionova E, Andreevskaya S, Kostrzewa M, Govorun V (2011) Mass spectrometry based methods for the discrimination and typing of mycobacteria. Infect Genet Evol 12: 838-845.
43. Sogawa K, Watanabe M, Sato K, Segawa S, Ishii C, Miyabe A, Murata S, Saito T, Nomura F (2011) Use of the MALDI BioTyper system with MALDI-TOF mass spectrometry for rapid identification of microorganisms. Anal Bioanal Chem 400: 1905-1911.
44. Springer B, Stockman L, Teschner K, Roberts GD, Bottger EC (1996) Two-laboratory collaborative study on identification of mycobacteria: molecular versus phenotypic methods. J Clin Microbiol 34: 296-303.
45. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PA, Kampfer P, Maiden MC, Nesme X, Rossello-Mora R, Swings J, Truper HG, Vauterin L, Ward AC, Whitman WB (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52: 1043-1047.
46. Stevenson LG, Drake SK, Murray PR (2010a) Rapid identification of bacteria in positive blood culture broths by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 48: 444-447.
47. Stevenson LG, Drake SK, Shea YR, Zelazny AM, Murray PR (2010b) Evaluation of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of clinically important yeast species. J Clin Microbiol 48: 3482-3486.
48. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4. 0. Mol Biol Evol 24: 1596-1599.
49. Telenti A, Marchesi F, Balz M, Bally F, Bottger EC, Bodmer T (1993) Rapid identification of mycobacteria to the species level by polymerase chain reaction and restriction enzyme analysis. J Clin Microbiol 31: 175-178.
50. van Veen SQ, Claas EC, Kuijper EJ (2010) High-throughput identification of bacteria and yeast by matrix-assisted laser desorption ionization-time of flight mass spectrometry in conventional medical microbiology laboratories. J Clin Microbiol 48: 900-907.
51. Verroken A, Janssens M, Berhin C, Bogaerts P, Huang TD, Wauters G, Glupczynski Y (2010) Evaluation of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of nocardia species. J Clin Microbiol 48: 4015-4021.
52. Zolg JW, Philippi-Schulz S (1994) The superoxide dismutase gene, a target for detection and identification of mycobacteria by PCR. J Clin Microbiol 32: 2801-2812.